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Microbiome analysis of healthy and diseased sponges Lubomirskia baicalensis by using cell cultures of primmorphs

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Microbiome analysis of healthy and diseased sponges Lubomirskia baicalensis by using cell cultures of primmorphs https://t.co/LdwlFlg1my https://t.co/wvylxiVLht
RT @host_microbe: Microbiome analysis of healthy and diseased sponges Lubomirskia baicalensis by using cell cultures of primmorphs https://…
Microbiome analysis of healthy and diseased sponges Lubomirskia baicalensis by using cell cultures of primmorphs https://t.co/w73SWTsMTh https://t.co/Caac1Y4lAR
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Supplemental Information

Samples of the healthy sponge and primmorphs

(A) The healthy freshwater Baikal sponge L. baicalensis, (B) cell culture of primmorphs of L. baicalensis obtained from the sponge. Scale bars are 5 mm. Canon EOS 200D digital camera.

DOI: 10.7287/peerj.preprints.27851v1/supp-1

Samples of diseased sponges

(A) The diseased freshwater Baikal sponge L. baicalensis. (B) The sick freshwater Baikal sponge L. baicalensis. Canon EOS 200D digital camera.

DOI: 10.7287/peerj.preprints.27851v1/supp-2

Experimental design study of the microbiomes of healthy, diseased sponges and primmorphs

Notes. 1 The suspensions of microorganisms from diseased sponge. 2 The suspensions of microorganisms from sick sponge.

DOI: 10.7287/peerj.preprints.27851v1/supp-3

Light and fluorescence images cell cultures of primmorphs of sponge L. baicalensis.

(A) Light microscopy, showing green microalgae located within amoebocytes in the healthy cell culture of primmorphs. Arrows show sponge amoebocytes within microalgae (B) Fluorescence microscopy, showing red autofluorescence of chlorophyll-containing intracellular of green algae in the healthy primmorphs. (C) The primmorphs infected with cellular suspension from the diseased sponge observed the death of green algae symbionts, sponge cell (indicated by arrow). Shown massive numbers, of different bacteria at 7 day (indicated by arrow). (D) Fluorescence microscopy, showing the death of microalgae (red color) in infected primmorphs from diseased sponge at 7 day. Bacteria shown blue color. (E) The primmorphs infected with cellular suspension from the diseased sponge for 21 days, shown residues of green algae in cell culture of primmorphs and huge biomass of bacteria (indicated by arrow). (F) Fluorescence microscopy showing death of green algae primmorphs infected suspension from the diseased sponge and massive of different bacteria for 21 day. Bacteria in infected primmorphs, shown blue color. Samples of primmorphs stained with the NucBlue Live ReadyProbes reagent for fluorescence microscopy. Scale bars: 10 μm.

DOI: 10.7287/peerj.preprints.27851v1/supp-4

SEM images of cell cultures of primmorphs

(A) The epithelial surface of healthy cultures were clean, flat and smooth. (B) The surface of the primmorphs infected with the cellular suspension from the diseased sponge. Observed melting of the epithelial cells of sponge, increased different bacteria at 7 day. (C) The primmorphs infected with cellular suspension from the diseased sponge, the death of green algae symbionts, sponge cells and massive growth of different bacteria for 21 day. (D) Bio-cake formed in infected cultures of primmorphs from diseased sponge at 30 day. Scale bars are 1 μm.

DOI: 10.7287/peerj.preprints.27851v1/supp-5

The alpha-diversity indexes ( Chao1 and Shannon index ) of the data distribution

A) The distribution between the group’s adult sponges and primmorphs. B) The distribution between the groups of healthy and diseased of sponges and primmorphs. Samples were referred to Table 1. We did not find significant differences between diversity the adult sponges and primmorphs by using Shannon index. The alpha-diversity indices (Shannon index) have significant difference between healthy and diseased groups (Table 3, Fig. 6 B).

DOI: 10.7287/peerj.preprints.27851v1/supp-6

The beta-diversity results of PCoA indicating the data distribution between groups

Samples of the healthy sponge and primmorphs are grouped into one cluster and differ significantly from the group of diseased. Samples were referred to Table 1.

DOI: 10.7287/peerj.preprints.27851v1/supp-7

Taxonomic profiles of the microbial communities at the phylum level

Relative abundance of reads assigned to phyla (to %). Samples were referred to Table 1.

DOI: 10.7287/peerj.preprints.27851v1/supp-8

Heatmap showing the family with significant differences of relative abundances amongst the two groups

Sample ID are referred to Table 1. Heatmap based on the scale of 0-8 log.

DOI: 10.7287/peerj.preprints.27851v1/supp-9

Samples of sponges L. baicalensis and cell culture of primmorphs

Samples were collected from the strait Olkhon Vorota, Lake Baikal.

DOI: 10.7287/peerj.preprints.27851v1/supp-10

Summary of microbial communities in sponges and primmorphs

Notes. The name of samples: SH (Healthy sponge); PH1 (Primmorphs for 1 day); PH14 (Primmorphs for 14 day); SD (Bleached sponge); PD (Primmorphs diseased); PID (Primmorphs infected by diseased sponge ); SS (Sick sponge); PIS (Primmorphs infected by sick sponge). Samples IDs are referred to Table 1.

DOI: 10.7287/peerj.preprints.27851v1/supp-11

The alpha-diversity indices (Сhao1, Shannon index)

The alpha-diversity were calculated using the QIIME2 software to establish the abundance and diversity of the sequences. Notes. Samples IDs are referred to Table 1.

DOI: 10.7287/peerj.preprints.27851v1/supp-12

Results pairwaise PERMANOVA test

Notes. Indicates p-value < 0.05.

DOI: 10.7287/peerj.preprints.27851v1/supp-13

Abundance and significant difference between the two groups at the phylum/family level

Notes. (to %). Colored lines indicate a shift in microbial communities in healthy and diseased groups.

DOI: 10.7287/peerj.preprints.27851v1/supp-14

Additional Information

Competing Interests

The authors declare there are no competing interests.

Author Contributions

Lubov Chernogor conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft, conceived and designed the experiments, contributed reagents/materials performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables.

Elizabet Klimenko performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft, pcontributed materials, performed the experiments.erformed the experiments.

Igor Khanaev performed the experiments, analyzed the data, approved the final draft, contributed materials, performed the experiments.

Sergei Belikov performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft, review & editing: reviewed drafts of the paper, visualization, analysis tools.

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

Raw sequencing data are available in the NCBI Sequence Read Archive under accession number PRJNA480187.

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA480187

Data Deposition

The following information was supplied regarding data availability:

Data is available in the NCBI Sequence Read Archive under accession number PRJNA480187 and PRJNA503292.

Funding

This study was funded by budget projects of Federal Agency of Scientific Organizations number 0345-2019-0002 and Russian Foundation for Basic research (RFBR) grant numbers: 16-04-00065; 16-54-150007; 18-04-00224. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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